Yesterday we reported that Google's link report dropped the number of links being reported across virtually all sites. Some have seen 70% drop in link counts as reported in Google Webmaster Tools.
A new Google Webmaster Help thread may have some more insight on what happened.
It seems that Google stopped reporting on the links pointing to your home page. Typically, but not always, your home page attracts the most amount of links. Now if Google stops reporting those home page links, then your link count may drop significantly.
If you login to Google Webmaster Tools and click on the "Links to Your Site" under "Traffic" and then view the "Your most linked content" you will notice your home page is not listed there. Strange, don't you think?
Google's John Mueller said in the thread that he thinks this is a display bug but needs to make sure. He wrote:
Thanks for the report, Anne (and thanks for escalating, Stevie!). This looks like an issue with how the data is displayed in Webmaster Tools, it shouldn't affect your site's crawling, indexing or ranking. I don't have any specifics at the moment, but the team is looking into the details to see what we can do here. Thanks for your patience & sorry for the confusion!
I hope to have an answer soon but it really seems like a bug and not a feature.
Forum discussion at Google Webmaster Help.